Biotin Protein Ligase

The attachment of biotin onto requiring proteins is catalysed by the ubiquitous enzyme biotin protein ligase (BPL), also known as the biotin inducible repressor, BirA, in E.coli and holocarboxylase synthase (HCS) in mammals. It was once believed a separate HCS existed for each of the carboxylases. However, with the availability of modern recombinant DNA technology and complete genome sequences, there is good evidence that only one biotin protein ligase is present in most bacteria, yeast and mammals. Arabidopsis thaliana and other plants species are a notable exception to this rule as they contain two HCS genes, one encoding a cytoplasmic enzyme and the other a chloroplast targeted enzyme.

Biotinylation is catalysed through a two-step reaction where biotin is first activated to biotinyl-5′-AMP in an ATP dependent manner. The biotin is then transferred onto the ε-amino group of a specific target lysine residue. The reaction mechanism is related to that of amino acyl-tRNA synthetases and lipoyl ligases where the reaction proceeds through the formation of an adenylated intermediate, suggesting a common ancestral relationship.

Of all the BPL’s, E.coli (BirA) is by far the most characterised and understood family member. A recent ensemble of BPL structures from the thermophilic archea Pirococcus Horikoshii OT3 have also provided new insights into the catalytic mechanism of BPLs.

BirA (35.5 kDa) contains three distinct domains that have been determined at 2.3 Å resolution in 1992 through X-ray crystallography in the unliganed form, apo_EcBPL. The monomeric structure measures 75 Å x 35 Å x 30 Å for the unliganded "apo" structure. The N-terminal 22-46 residues adopt a helix-turn-helix motif, a structure associated with DNA binding proteins. The central domain consists of five α helices, 7 strands of mixed β-sheets as well as four poorly-defined loops that appear in pairs in the 3D structure. These loops consist of residues 110-128, 212-233 and 140 146 and 193-199. The C- terminus consists of 6 strands which form a β-sandwich that seals the end of the enzyme and has been found to function in the transfer of biotin onto BCCP. Upon biotin binding, the protein homodimerises and the unstructured loops become more ordered.

Additional Resources
For additional information, see: Carbohydrate Metabolism

3D structures of Biotin Protein Ligase
3l1a, 3l2z, 2cgh – BPL – Mycobacterium tuberculosis

2ej9 – BPL – Methanocaldococcus jannaschii

2e64, 2e65, 2e1h, 2e10, 2dzc, 2hni - PhBPL (mutant) – Pyrococcus horikoshii

3fjp, 2eay – AaBPL – Aquifex aeolicus

3efr – AaBPL (mutant)

1bia – BPL – Escherichia coli

Biotin protein ligase binary complex
3efs – AaBPL + ATP + biotin

2ejf, 2ejg – PhBPL (mutant) + methylmalonyl-CoA decarboxylase γ chain

2e41 - PhBPL (mutant) + product analog

1x01 - PhBPL + ATP

1wqw - PhBPL + biotinyl-AMP

2dz9, 2dxu, 2dve, 2dti, 2djz, 2deq - PhBPL (mutant) + biotinyl-AMP

Biotin protein ligase ternary complex
2zgw - PhBPL (mutant) + adenosine + biotin

2dxt - PhBPL (mutant) + ATP + biotin

2dto, 2dth, 2fyk - PhBPL + ATP + biotin

2dkg - PhBPL + biotinyl-AMP + pyrophosphate